Ex Parte Shannon et al

Board of Patent Appeals and Interferences

May 26, 2010

10877231 (B.P.A.I. May. 26, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte KAREN W. SHANNON, PAUL K. WOLBER,
GLENDA C. DELENSTARR, PETER G. WEBB and
ROBERT H. KINCAID
__________

Appeal 2009-007998
Application 10/877,231
Technology Center 1600
__________

Decided: May 26, 2010
__________

Before DEMETRA J. MILLS, FRANCISCO C. PRATS and
MELANIE L. McCOLLUM, Administrative Patent Judges.

MILLS, Administrative Patent Judge.

DECISION ON APPEAL

This is an appeal under 35 U.S.C. § 134. The Examiner has rejected
the claims for anticipation and obviousness. We have jurisdiction under 35
U.S.C. § 6(b).

Appeal 2009-007998
Application 10/877,231

STATEMENT OF THE CASE
The following claims are representative:
1. A method for producing an array comprising:
receiving one or more target polynucleotide sequences;
determining an evaluated probe set for each of said one or more target
polynucleotide sequences, wherein said evaluated probe set comprises
oligonucleotide sequences;
outputting data relating to the oligonucleotide sequences of said
evaluated probe set for each of said one or more target polynucleotide
sequences; and
fabricating an array from said outputted data.

2. A method for producing an array comprising:
receiving one or more target polynucleotide sequences;
determining an evaluated probe set for each of said one or more target
polynucleotide sequences, wherein said evaluated probe set comprises
oligonucleotide sequences;
outputting data relating to the oligonucleotide sequences of said
evaluated probe set for each of said one or more target polynucleotide
sequences to a user for examination and modification, as desired to produce
a final output data set; and
fabricating an array from said final output data set.

4. The method according to Claim 2, wherein said method is performed
at a first computer and said method further comprises communicating said
outputted data with a second computer.

7. A system for fabricating an array, said system comprising:
an input device for receiving one or more target polynucleotide
sequences;
a means for determining an evaluated probe set for each of said one or
more target polynucleotide sequences, wherein said evaluated probe set
comprises oligonucleotide sequences;
a communication means for outputting data relating to the
oligonucleotide sequences of said evaluated probe set for each of said one or
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more target polynucleotide sequences to a user for examination and
modification, as desired to produce a final output data set; and
means for fabricating an array from said final output data set.

8. The system according to Claim 7, wherein said system comprises a first
computer, and wherein said communication means communicates with a
second computer.

11. A method for providing custom probe arrays, comprising the acts of:
receiving a user selection of one or more probe set identifiers that
each identify a plurality of potential probes;
determining verified probe sets of verified probes corresponding to
the one or more probe set identifiers;
generating a custom probe array design based, at least in part, upon
the verified probe sets; and
providing to the user one or more probe arrays based on the probe
array design.

12. A method for providing custom probe arrays, comprising the acts of:
receiving a user selection of one or more probe set identifiers that
identify one or more potential probes;
determining verified probe sets of verified probes corresponding to
the probe set identifiers;
generating a custom probe array design based, at least in part, upon
the verified probe sets;
enabling for display to the user a representation of one or more
aspects of the custom probe array design via one or more computer
programs enabled to receive a user selection specifying acceptance,
modification, or rejection of the custom probe array design; and
providing to the user one or more probe arrays based on the probe
array design and responsive to the user specification of acceptance or
modification.

14. The method of claim 12, wherein: the user selection is received over the
Internet.

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Grounds of Rejection
1. “Claims 1-6 and 18 are rejected under 35 U.S.C. [§] 102(e) as being
anticipated by Lockhart”1 (Ans. 3).
2. “Claims 7-10 are rejected under 35 U.S.C. [§] 103(a) as being
unpatentable over Lockhart” (id. at 7).
3. Claims 11-13, 15-16, 19, 21-22, and 24 are rejected under 35 U.S.C.
§103(a) as being unpatentable over Sullivan2 in view of Southern3 (id. at 9).
4. Claims 14, 17, 20 and 23 are rejected under 35 U.S.C. § 103(a) as being
unpatentable over Sullivan in view of Southern and Anderson4 (id. at 14).
Appellants separately argue claims 2, 4, 7, 8, 11, 12 and 14. (App. Br.
8-9.)

ADDITIONAL FINDINGS OF FACT
The Examiner’s fact finding is set forth in the Answer on pages 4-15.
We adopt the Examiner’s fact finding and analysis as our own, and provide
the following additional comments and facts.
1. The Specification does not define the term “evaluated probe set.”
(Claim 1.)
2. “Evaluate”5 means 1) to determine or fix the value of; or 2) to
examine carefully.

1 Lockhart et al., US 6,344,316 B1, issued Feb. 5, 2002
2 Sullivan et al., US 5,616,488, issued Apr. 1, 1997
3 E.M. Southern et al., Arrays of complementary oligonucleotides for
analysing the hybridisation behaviour of nucleic acids, 22 NUCLEIC ACIDS
RESEARCH 1368-1373 (1994).
4 Anderson, US 6,456,942 B1, issued Sep. 24, 2002
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3. The term “verify” means to “ascertain the truth or correctness of,
as by examination, research, or comparison.” (Reply Br. 4.)

Anticipation and Obviousness Lockhart
1. “Claims 1-6 and 18 are rejected under 35 U.S.C. [§]102(e) as being
anticipated by Lockhart” (Ans. 3).
2. “Claims 7-10 are rejected under 35 U.S.C. [§]103(a) as being
unpatentable over Lockhart” (id. at 7).

ISSUE
The Examiner argues that Lockhart teaches/renders obvious each
element claimed.
Appellants contend “the claimed evaluated probe set for one or more
received target polynucleotide[s] …does not encompass randomly
generated/selected probe sets as taught in Lockhart.” (App. Br. 11.)
The issue is: Does Lockhart support the Examiner’s
anticipation/obviousness rejection providing for an “evaluated probe set” as
claimed? (Claim 1.)

PRINCIPLES OF LAW
The interpretation of terms in a claim is a matter of law. In re
American Academy Of Science Tech Center, 367 F.3d 1359, 1363 (Fed. Cir.

5 Websters II New Riverside Dictionary, page 447, the Riverside Publishing
Co, Boston, MA (1994).

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2004). “It is axiomatic that, in proceedings before the PTO, claims in an
application are to be given their broadest reasonable interpretation consistent
with the specification.” In re Sneed, 710 F.2d 1544, 1548 (Fed. Cir. 1983).
“Without evidence in the patent specification of an express intent to impart a
novel meaning to a claim term, the term takes on its ordinary meaning.”
Optical Disc Corp. v. Del Mar Avionics, 208 F.3d 1324, 1334 (Fed. Cir.
2000).
In order for a prior art reference to serve as an anticipatory reference,
it must disclose every limitation of the claimed invention, either explicitly or
inherently. See In re Schreiber, 128 F.3d 1473, 1477 (Fed. Cir. 1997).
“In rejecting claims under 35 U.S.C. § 103, the examiner bears the
initial burden of presenting a prima facie case of obviousness. Only if that
burden is met, does the burden of coming forward with evidence or
argument shift to the applicant.” In re Rijckaert, 9 F.3d 1531, 1532 (Fed.
Cir. 1993) (citations omitted). In order to determine whether a prima facie
case of obviousness has been established, we consider the factors set forth in
Graham v. John Deere Co., 383 U.S. 1, 17 (1966): (1) the scope and content
of the prior art; (2) the differences between the prior art and the claims at
issue; (3) the level of ordinary skill in the relevant art; and (4) objective
evidence of nonobviousness, if present.
When evaluating claims for obviousness, “the prior art as a whole
must be considered. The teachings are to be viewed as they would have
been viewed by one of ordinary skill.” In re Hedges, 783 F.2d 1038, 1041
(Fed. Cir. 1986). Thus, “‘[i]t is impermissible within the framework of
section 103 to pick and choose from any one reference only so much of it as
will support a given position, to the exclusion of other parts necessary to the
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full appreciation of what such reference fairly suggests to one of ordinary
skill in the art.’” Id. (quoting In re Wesslau, 353 F.2d 238, 241 (CCPA
1965)).
In In re Venner, the court held that broadly providing an automatic or
mechanical means to replace a manual activity which accomplished the
same result is not sufficient to distinguish over the prior art. In re Venner,
262 F.2d 91, 95 (CCPA 1958).

ANALYSIS
Anticipation
Claim 1
Appellants contend that “the claimed evaluated probe set for one or
more received target polynucleotide[s] …does not encompass randomly
generated/selected probe sets as taught in Lockhart.” (App. Br. 11)(emphasis
added.)
We essentially agree with the Examiner’s fact finding, statement of
the rejection, and responses to the Appellants’ argument. We provide the
following additional comment.
Appellants have not defined the term “evaluated probe set” in the
Specification. (Claim 1.) Thus, we turn to the ordinary meaning of the term
“evaluate.” To “evaluate” means 1) to determine or fix the value of; or 2) to
examine carefully.
Lockhart states:
[T]he methods of identifying differences in nucleic acid levels
between two or more nucleic acid samples involve the steps of: (a)
providing one or more oligonucleotide arrays each comprising probe
oligonucleotides wherein said probe oligonucleotides comprise a
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nucleotide sequence or subsequences selected according to a process
selected from the group consisting of a random selection, a haphazard
selection, a nucleotide composition biased selection, and all possible
oligonucleotides of a preselected length.

(Lockhart, col. 3, ll. 48-56.)(emphasis added.)

We agree with the Examiner that when, as described in Lockhart, a
nucleotide composition is a biased selection, or all possible oligonu-
cleotides are of a preselected length, that the oligonucleotide probe sets have
been selected and/or examined carefully in accordance with the definition of
“evaluated,” as claimed. (Id.) In other words, Lockhart selects, determines,
or fixes the value of probes by choosing probe sets based upon a preselected
length, or biased in some other manner. Appellants have not provided
convincing evidence to the contrary.

Claims 2, 3, 5, 6, and 18
We adopt the Examiner’s analysis of these claims as our own and
provide the following additional comment. In particular, with respect to
claim 2, Appellants further argue that Lockhart does not disclose the
limitation of claim 2, “outputting data relating to the oligonucleotides of the
evaluated probe set . . . to a user for examination and modification, as
desired to produce a final output set.” (App. Br. 12.)
The Examiner finds that the data from Table 2 of Lockhart is
outputted to a user because the Table presents data that is in fact used to
generate the arrays of Example I of Lockhart in steps B and C. (Ans. 5.) As
the Examiner points out (Ans. 16-17), the recitation “for examination and
modification” in claim 2 does not require any affirmative action on the part
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of the user. On this basis, we find that Lockhart teaches the “outputting
data” limitation of claim 2.

Claim 4
Appellants contend that claim 4 is not anticipated by Lockhart
because Lockhart only discloses one computer and does not disclose a
second computer with which output data is communicated. (App. Br. 13-
14.)
Although we agree with the Examiner that Lockhart discloses
multiple computers (Ans. 6.), we do not find that the Examiner has
indicated, in an anticipatory fashion, where array fabrication output data,
rather than hybridization data, is communicated to a second computer. The
anticipation rejection of claim 4 is reversed.

Obviousness
Claims 7-10
Regarding claim 7, the Examiner acknowledges that Lockhart does
not explicitly state that a computer is employed to analyze the data involved
in fabricating an array. (Ans. 8.) However, Lockhart does disclose a
computer system in Fig. 6 and use of a multiprocessor in Fig. 7. Thus the
Examiner finds that it would have been obvious to use the computer in
Lockhart to assist in fabricating arrays for the purpose of automating the
building of arrays since automation streamlines the claimed processes.
(Ans. 9.)
We agree that automation of the process of fabricating arrays would
have been obvious. In re Venner, 262 F.2d at 95. As discussed above,
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Lockhart discloses that its arrays can be prepared according to specific
criteria, including nucleotide bias and oligonucleotide length (Lockhart, col.
3, ll. 48-56), and we detect no error in the Examiner’s finding that an
ordinary artisan would have found computer assistance useful in preparing
arrays according to that criteria.
With respect to claim 8, we reference the Examiner’s finding in the
Answer at page 8 (characterizing Lockhart at column 61, lines 45-76, as
describing “a single computer [which] performs an analysis and is able to
communicate with a plurality of other computers”) and adopt that as our
own.
Therefore, we find that Lockhart discloses the claimed system for
producing an array.

CONCLUSION OF LAW
We agree with the Examiner’s conclusion that the claims are
anticipated/rendered obvious by Lockhart, as Lockhart discloses an
evaluated probe set. The anticipation and obviousness rejections over
Lockhart are affirmed, except as to claim 4, for the reasons discussed.

Obviousness -- Sullivan and Southern
3. Claims 11-13, 15-16, 19, 21-22, and 24 are rejected under 35 U.S.C.
§103(a) as being unpatentable over Sullivan in view of Southern. (Ans. 9.)
4. Claims 14, 17, 20 and 23 are rejected under 35 U.S.C. § 103(a) as being
unpatentable over Sullivan in view of Southern and Anderson. (Id. at 14.)

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ISSUE
The Examiner finds that Sullivan and Southern teach the step of
determining “verified probe sets,” as claimed. (Claim 11.)
Appellants contend that the cited references fail to disclose a step of
determining “verified probe sets,” as claimed. (App. Br. 18-20.)
The primary issue is: Does the combination of Sullivan and Southern
support the Examiner’s conclusion that they teach a step of determining
“verified probe sets,” as claimed?

ANALYSIS
We essentially agree with the Examiner’s fact finding, statement of
the rejection, and responses to the Appellants’ argument and provide the
following additional comment.
Appellants contend that the cited references fail to disclose a step of
determining “verified probe sets,” as claimed (id.). We are not persuaded.
In particular, the Examiner finds that:
The patent of Sullivan et al. illustrates a probe set identifier of a
target sequence in Figure 1 as "NNNNUHNNNNNN". This sequence
identifier corresponds to the plurality of probes (i.e. probe sets) listed
in Table II of Sullivan et al. (columns 11-14). The sequences are
verified by comparing the individual sequences with the sequence
identifier shown in the schematic of Figure 1. Table II is interpreted
to serve as a basis for the probe array design.

(Ans. 10.)
According to Appellants, the term “verify” means to “ascertain the
truth or correctness of, as by examination, research, or comparison.” (Reply
Br. 4.)
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The finding of the Examiner that Sullivan teaches a step of comparing
a probe set identifier to a target sequences as in Figure 1, is described in the
excerpt reproduced above. Thus, by setting forth the generic structure of the
sequence of interest in Figure 1, and comparing the sequences of the set of
generated probes to that structure (see Table II of Sullivan), Sullivan meets
the limitation of verifying the probe set or comparing a probe to a desired
target sequence, as in claim 11. Appellants have provided no convincing
evidence to the contrary.

Claim 12
Claim 12 recites a method for providing custom probe array including
a step of “enabling for display to the user a representation of one or more
aspects of the custom probe array design via one or more computers enabled
to receive a user selection specifying acceptance, modification, or rejection
of the custom probe array design.”
The Examiner acknowledges that Sullivan does not explicitly describe
the generation of an array using outputted data. (Final Rej. 12.) The
Examiner reasons, however, that the claim term “enabling” is an intended
use that does not require the claim’s practitioner to actually display the data,
but instead only to allow its display in the claimed fashion (Ans. 19).
The Examiner finds that Sullivan discloses figures which are
generated by computer and computer programs. These programs may be
altered by user selection. (Id. at 11.) In particular, Sullivan engineered
ribozyme motifs which were designed to be directed against IL-5. The
designed ribozymes were selected and tested for function by analyzing IL-5
expression. (Sullivan, col. 8, ll. 50-58.) The Examiner finds that Figs. 1-6,
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Tables I-V of Sullivan demonstrate displays of engineered ribozyme data.
Thus, Sullivan enables the receipt of input from a user specifying
modification or acceptance of the probe array design. (Ans. 19-20.) In other
words, once the user determines the probe array which is desired in Sullivan
he can select or accept the array and automate it as described in Southern.
The Examiner relies on Southern for the disclosure of the detailed
process by which arrays are fabricated. (Southern, 1369, col. 2, ll. 23-50;
Figs 2 and 3.) (Ans. 11.) In Southern, the automated synthesizer (ABI 381
A) detailed in the description of Fig. 1, is programmed to couple bases in the
order to complement the target sequence. (Southern, 1369, col. 2, ll. 23-50.)
The Examiner finds that “It would have been obvious to someone of
ordinary skill in the art at the time of the instant invention to modify the
probe set identification method of Sullivan et al. by use of the array
fabrication method of Southern et al. because Southern et al. has the
advantage of generating arrays (i.e. those disclosed in Sullivan et al.) for the
purpose of mutation analysis.” (Final. Rej. 16.) (Southern, page 1373, col.
2, ll. 6-8.) These disclosures in the combined references would have
reasonably supported the rejection of claim 12.

Claim 14
Appellants present the same argument in claim 14 as for claim 12.
(App. Br. 22.) Claim 14 falls for the same reason as claim 12. With respect
to Appellants’ argument that Anderson fails to teach use of a network or the
internet, see Anderson Figs. 1 and 2. (Ans. 14-15.)
We accept the Examiner’s responses and fact finding to remaining
claims not discussed herein.
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The obviousness rejections over Sullivan in view of Southern are
affirmed.

SUMMARY
The anticipation and obviousness rejections are affirmed, except the
anticipation rejection of claim 4 is reversed.

TIME PERIOD
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED-IN-PART

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